My favourite would be Metal Gear Solid 2: Sons of Liberty. It features a damn fine gameplay without overburdening it with too many things, an impressive score worth listening everytime, a meta-commentary that surpasses every single other game in the franchise and an amazing story that would later be the pivotal point of the whole saga (Even with MGS4's persistence of retconning some aspects of it).
On the negative side, I guess the bosses are alright but don't hold a candle to those in MGS3, and the E.E. escort sequence isn't bad but can be too damn frustrating on higher difficulties.







